The 7.3 is a good truck, no doubt. I have heard horror stories on the 6.0 also, but then a lot of others swear by them. If you are looking between 2001-2003 anyways though, your probably going to get a 7.3L anyways. The 6.0L's started at the end of 03. As far as manual or automatic tranny, its up to you. Diesels put out a lot of torque, so I typically figure I might be able to save myself some proble4ms by going with a manual tranny. Plus, I love shifting!
Anyways, good luck with your search, and let us know if we can help any further!